Hi all,
I came across one problem with RDKit today, namely Chem.PathToSubmol()
function. Does the "path" mean atom or bond indices? On this very list I
fount the examples showing usage with atom idx [
https://www.mail-archive.com/[email protected]/msg03966.html],
while the example on "Getting started in python" is feeding
Chem.FindAtomEnvironmentOfRadiusN() which gives a list of bond indices. The
documentation could be more explicit here... After my brief analysis of the
code I found out that the bonds should be used (correct me if I'm wrong).
So here comes the question: is there an equivalent function or a clever way
to do Chem.PathToSubmol() on atom indices? Currently I do: 1) get the atom
path; 2) get bonds between every atom in path (their indices); 3) get
submol with Chem.PathToSubmol()
PS.
I use it to get each proteins residue (amino acid) in separate mol. It
would be much easier if we could use "Molecule -> Residues -> Atoms"
instead of "Molecule -> Atoms -> (grouping of monomers) -> Residues".
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
[email protected]
------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
